05.X. Object oriented programming in a nutshell

Recap: Data structures in R

Motivation for “Objects”

• Real “items” are more complext than just a dataframe:
  • Think of designing an informatics system for a hospital
    • You have many patients
    • Patients have a lot of attributes
      • Name, Height, Weight → Can store it in a row of a data frame
      • Medication history, CT-scans → Cannot store it in a row of a data frame
• → A new way of storing is needed an: object
• In a very simple way, you can think of it as a list on steroids.

Patient is class of object with concrete instances, like poor John

• Class is a type of object: Think of patients and doctors in the hospital.
• Instance is a concrete example

Calculate BMI from 2 other attributes

BMI is a new attribute of “patient”

Motivation for “Object oriented programming”

• If you always handle the same kind of objects, you can design the functions to work specifically with those objects!
  • Write a simple function for BMI: calc_BMI()
    • calc_BMI(Weight, Height)
  • But you know that all patients have these attribute, so you could write a simple function
    • calc_BMI(Patient)
  • This function can put back the BMI immediately to the object Patient.
  • These functions for object are called methods.

Methods are functions designed to work with a type of object.

• A method is a function designed for a particular type of object.
• Most Seq-data analysis packages work with R
  • Imagine a function like
    • Cell_quality(SingleCellObject)
    • Cluster_SC(SingleCellObject)

Object oriented programming in R

• S4 objects (there are other kinds)
• Subset the elements by the @ character

References:

http://adv-r.had.co.nz/S3.html

http://adv-r.had.co.nz/S4.html

Take home messages for object oriented programming

• Life is too complex for a data frame → invention of objects.
  • Type of object is called class.
  • An example of that class is called instance.
• Writing functions to work with objects, called methods.